If someone's still looking for a suggestion to the problem that @Ponleu and @David Schilling have described here (regarding content that goes above the FlatList), then this is the approach I took:

<SafeAreaView style={{flex: 1}}>
    <FlatList
      data={data}
      ListHeaderComponent={ContentThatGoesAboveTheFlatList}
      ListFooterComponent={ContentThatGoesBelowTheFlatList} />
</SafeAreaView>

You can read more about this here: https://facebook.github.io/react-native/docs/flatlist#listheadercomponent

Hopefully it helps someone. :)

Just in case this helps someone, this is how I fixed the error in my case.

I had a FlatList nested inside a ScrollView:

render() {
    return (
        <ScrollView>
            <Text>{'My Title'}</Text>
            <FlatList
                data={this.state.myData}
                renderItem={({ item }) => {
                    return <p>{item.name}</p>;
                }}
            />
            {this.state.loading && <Text>{'Loading...'}</Text>}
        </ScrollView>
    );
}

and I got rid of the ScrollView by using the FlatList to render everything I needed, which got rid of the warning:

render() {
    const getHeader = () => {
        return <Text>{'My Title'}</Text>;
    };

    const getFooter = () => {
        if (this.state.loading) {
            return null;
        }
        return <Text>{'Loading...'}</Text>;
    };

    return (
        <FlatList
            data={this.state.myData}
            renderItem={({ item }) => {
                return <p>{item.name}</p>;
            }}
            ListHeaderComponent={getHeader}
            ListFooterComponent={getFooter}
        />
    );
}

The best way is to disable that warning because sometimes Flatlist need to be in ScrollView.

UPDATE RN V0.63 ABOVE

YellowBox is now changed and replace with LogBox

FUNCTIONAL

import React, { useEffect } from 'react';
import { LogBox } from 'react-native';

useEffect(() => {
    LogBox.ignoreLogs(['VirtualizedLists should never be nested']);
}, [])

CLASS BASED

import React from 'react';
import { LogBox } from 'react-native';

componentDidMount() {
    LogBox.ignoreLogs(['VirtualizedLists should never be nested']);
}

UPDATE RN V0.63 BELOW

FUNCTIONAL

import React, { useEffect } from 'react';
import { YellowBox } from 'react-native';

useEffect(() => {
    YellowBox.ignoreWarnings(['VirtualizedLists should never be nested']);
}, [])

CLASS BASED

import React from 'react';
import { YellowBox } from 'react-native';

componentDidMount() {
    YellowBox.ignoreWarnings(['VirtualizedLists should never be nested']);
}